Summary
Serotonin (5-HT) neurotransmitter transporter, N-terminus
No Pfam abstract.
InterPro entry IPR013086
Neurotransmitter transport systems are integral to the release, re-uptake and recycling of neurotransmitters at synapses. High affinity transport proteins found in the plasma membrane of presynaptic nerve terminals and glial cells are responsible for the removal from the extracellular space of released-transmitters, thereby terminating their actions PUBMED:15336049. Plasma membrane neurotransmitter transporters fall into two structurally and mechanistically distinct families. The majority of the transporters constitute an extensive family of homologous proteins that derive energy from the co-transport of Na+ and Cl-, in order to transport neurotransmitter molecules into the cell against their concentration gradient. The family has a common structure of 12 presumed transmembrane helices and includes carriers for gamma-aminobutyric acid (GABA), noradrenaline/adrenaline, dopamine, serotonin, proline, glycine, choline, betaine and taurine. They are structurally distinct from the second more-restricted family of plasma membrane transporters, which are responsible for excitatory amino acid transport. The latter couple glutamate and aspartate uptake to the cotransport of Na+ and the counter-transport of K+, with no apparent dependence on Cl- PUBMED:8811182. In addition, both of these transporter families are distinct from the vesicular neurotransmitter transporters PUBMED:8103691, PUBMED:7823024.
Sequence analysis of the Na+/Cl- neurotransmitter superfamily reveals that it can be divided into four subfamilies, these being transporters for monoamines, the amino acids proline and glycine, GABA, and a group of orphan transporters PUBMED:9779464.
The serotonin (5-HT) neurotransmitter transporter is known to be expressed in the brain and also in the periphery: on platelet, placental and pulmonary cell membranes. The brain 5-HT transporter is thought to be the principal site of action of therapeutic anti-depressants (which inhibit this transporter), and it may also mediate the behavioural effects of cocaine and amphetamines PUBMED:7681602. The human form (630 amino acids) is 92% identical to the rat brain 5-HT transporter, and shares the same predicted topology and conserved sites for post-translational modification.
This domain is found at the N-terminal region of some 5-HT neurotransmitters.
Gene Ontology
| Cellular component | integral to plasma membrane (GO:0005887) |
| Molecular function | serotonin:sodium symporter activity (GO:0005335) |
| Biological process | neurotransmitter transport (GO:0006836) |
External database links
| PANDIT: | PF03491 |
| SYSTERS: | 5HT_transporter |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Alignments
There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...
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Formatting options
Download options
Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.
You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.
External links
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER2.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed or full alignments.
Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | PRINTS |
| Previous IDs: | none |
| Type: | Family |
| Author: | Griffiths-Jones SR |
| Number in seed: | 3 |
| Number in full: | 23 |
| Average length of the domain: | 35.60 aa |
| Average identity of full alignment: | 78 % |
| Average coverage of the sequence by the domain: | 7.98 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq
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| Model details: |
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| Model length: | 42 | ||||||||||||
| Family (HMM) version: | 6 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
Tree controls
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